align_compare.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Prot_pos.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/general/Object_id.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <algo/align/util/align_compare.hpp>
#include <algo/align/util/score_lookup.hpp>
#include <algo/align/util/algo_align_util_exceptions.hpp>
#include <corelib/rwstream.hpp>
#include <util/checksum.hpp>
#include <cmath>
#include <ctype.h>

Include dependency graph for align_compare.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
struct	SComparison
struct	SAlignment_PtrLess
struct	SComp_Less

Typedefs
typedef set< CAlignCompare::SAlignment *, SAlignment_PtrLess >	TAlignPtrSet
typedef pair< CAlignCompare::SAlignment *, CAlignCompare::SAlignment * >	TPtrPair
typedef pair< TPtrPair, SComparison >	TComp

Functions
	USING_SCOPE (objects)
bool	s_IsOverlapping (CAlignCompare::SAlignment const *lhs, CAlignCompare::SAlignment const *rhs, CAlignCompare::ERowComparison row)
static void	s_UpdateSpans (const TSeqRange &query_range, const TSeqRange &subject_range, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
static void	s_GetAlignmentSpans_Interval (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
static void	s_GetAlignmentMismatches (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
static void	s_GetAlignmentSpans_Exon (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
static void	s_GetAlignmentSpans_Intron (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
static void	s_GetAlignmentSpans_Span (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row)
template<typename T >
void	s_PopulateScores (const CSeq_align &align, const vector< string > &score_list, vector< T > &scores, bool required=true)
static void	s_PopulateScoreSet (const CSeq_align &align, const set< string > &score_set, bool score_set_as_blacklist, CAlignCompare::TIntegerScoreSet &integer_scores, CAlignCompare::TRealScoreSet &real_scores)
static bool	s_EquivalentScores (const CAlignCompare::TRealScoreSet &scores1, const CAlignCompare::TRealScoreSet &scores2, double real_score_tolerance)
static void	s_PopulateExtSet (const CSeq_align &align, const set< string > &ext_set, bool ext_set_as_blacklist, CAlignCompare::TExtSet &exts)
string	s_ConvertToHexString (unsigned char *ptr, unsigned int length)
static bool	s_EquivalentExts (const CAlignCompare::TExtSet &exts1, const CAlignCompare::TExtSet &exts2)

Typedef Documentation

TAlignPtrSet

typedef set<CAlignCompare::SAlignment *, SAlignment_PtrLess> TAlignPtrSet

Definition at line 659 of file align_compare.cpp.

TComp

typedef pair<TPtrPair, SComparison> TComp

Definition at line 661 of file align_compare.cpp.

TPtrPair

typedef pair<CAlignCompare::SAlignment *, CAlignCompare::SAlignment *> TPtrPair

Definition at line 660 of file align_compare.cpp.

Function Documentation

s_ConvertToHexString()

string s_ConvertToHexString	(	unsigned char *	ptr,
		unsigned int	length
	)

Definition at line 476 of file align_compare.cpp.

References i, and NStr::NumericToString().

Referenced by s_EquivalentExts().

s_EquivalentExts()

static bool s_EquivalentExts ( const CAlignCompare::TExtSet &  exts1, const CAlignCompare::TExtSet &  exts2  )

static

Definition at line 489 of file align_compare.cpp.

References map_checker< Container >::begin(), CChecksum::eMD5, map_checker< Container >::end(), CChecksumStreamWriter::GetChecksum(), CChecksum::GetMD5Digest(), MSerial_AsnBinary, and s_ConvertToHexString().

Referenced by SComparison::SComparison().

s_EquivalentScores()

static bool s_EquivalentScores ( const CAlignCompare::TRealScoreSet &  scores1, const CAlignCompare::TRealScoreSet &  scores2, double  real_score_tolerance  )

static

Definition at line 425 of file align_compare.cpp.

References abs, map_checker< Container >::begin(), map_checker< Container >::end(), and max().

Referenced by SComparison::SComparison().

s_GetAlignmentMismatches()

static void s_GetAlignmentMismatches ( const CSeq_align &  align, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 148 of file align_compare.cpp.

References CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CAlignCompare::e_Query, CAlignCompare::e_Subject, eNa_strand_minus, eUnknown, CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CSeq_align_Base::C_Segs::GetSpliced(), isdigit(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, lookup(), match(), max(), min(), NCBI_THROW, CAlignCompare::SAlignment::query_mismatches, row, and CAlignCompare::SAlignment::subject_mismatches.

Referenced by CAlignCompare::SAlignment::SAlignment().

s_GetAlignmentSpans_Exon()

static void s_GetAlignmentSpans_Exon ( const CSeq_align &  align, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 277 of file align_compare.cpp.

References CProduct_pos::AsSeqPos(), CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, eUnknown, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CStd_seg_Base::GetLoc(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqRange(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, NCBI_THROW, row, s_UpdateSpans(), CRange_Base::SetFrom(), CRange_Base::SetTo(), and CSeq_align_Base::C_Segs::Which().

Referenced by CAlignCompare::SAlignment::SAlignment().

s_GetAlignmentSpans_Interval()

static void s_GetAlignmentSpans_Interval ( const CSeq_align &  align, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 81 of file align_compare.cpp.

References ConvertSeqAlignToPairwiseAln(), CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Std, eUnknown, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::GetStd(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsNull(), ITERATE, NCBI_THROW, r(), r0, r1, row, s_UpdateSpans(), and CSeq_align_Base::C_Segs::Which().

Referenced by CAlignCompare::SAlignment::SAlignment().

s_GetAlignmentSpans_Intron()

static void s_GetAlignmentSpans_Intron ( const CSeq_align &  align, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 325 of file align_compare.cpp.

References CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_seg_Base::CanGetProduct_strand(), eUnknown, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg_Base::GetProduct_strand(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, NCBI_THROW, row, s_UpdateSpans(), CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by CAlignCompare::SAlignment::SAlignment().

s_GetAlignmentSpans_Span()

static void s_GetAlignmentSpans_Span ( const CSeq_align &  align, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 361 of file align_compare.cpp.

References CSeq_align::GetSeqRange(), row, and s_UpdateSpans().

Referenced by CAlignCompare::SAlignment::SAlignment().

s_IsOverlapping()

bool s_IsOverlapping	(	CAlignCompare::SAlignment const *	lhs,
		CAlignCompare::SAlignment const *	rhs,
		CAlignCompare::ERowComparison	row
	)

Definition at line 1282 of file align_compare.cpp.

References CAlignCompare::e_Query, CAlignCompare::e_Subject, COpenRange< Position >::IntersectingWith(), CAlignCompare::SAlignment::query_range, row, and CAlignCompare::SAlignment::subject_range.

Referenced by CAlignCompare::NextGroup().

s_PopulateExtSet()

static void s_PopulateExtSet ( const CSeq_align &  align, const set< string > &  ext_set, bool  ext_set_as_blacklist, CAlignCompare::TExtSet &  exts  )

static

Definition at line 448 of file align_compare.cpp.

References set< Key, Compare >::empty(), eUnknown, CSeq_align_Base::GetExt(), CSeq_align_Base::IsSetExt(), ITERATE, NCBI_THROW, map_checker< Container >::size(), and set< Key, Compare >::size().

Referenced by CAlignCompare::SAlignment::SAlignment().

s_PopulateScores()

template<typename T >

void s_PopulateScores	(	const CSeq_align &	align,
		const vector< string > &	score_list,
		vector< T > &	scores,
		bool	required = true
	)

Definition at line 369 of file align_compare.cpp.

References CAlgoAlignUtilException::eScoreNotFound, CException::GetErrCode(), ITERATE, lookup(), T, and rapidjson::value.

Referenced by CAlignCompare::SAlignment::SAlignment().

s_PopulateScoreSet()

static void s_PopulateScoreSet ( const CSeq_align &  align, const set< string > &  score_set, bool  score_set_as_blacklist, CAlignCompare::TIntegerScoreSet &  integer_scores, CAlignCompare::TRealScoreSet &  real_scores  )

static

Definition at line 389 of file align_compare.cpp.

References CSeq_align_Base::GetScore(), CSeq_align_Base::IsSetScore(), ITERATE, lookup(), and rapidjson::value.

Referenced by CAlignCompare::SAlignment::SAlignment().

s_UpdateSpans()

static void s_UpdateSpans ( const TSeqRange &  query_range, const TSeqRange &  subject_range, CAlignCompare::SAlignment &  align_info, CAlignCompare::ERowComparison  row  )

static

Definition at line 72 of file align_compare.cpp.

References CAlignCompare::e_Query, CAlignCompare::e_Subject, row, and CAlignCompare::SAlignment::spans.

Referenced by s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentSpans_Intron(), and s_GetAlignmentSpans_Span().

USING_SCOPE()

USING_SCOPE

(

objects

)